In Sign of Normalization, Pentagon to Reimburse Pakistan $688 Million

WASHINGTON — The Pentagon quietly notified Congress this month that it would reimburse Pakistan nearly $700 million for the cost of stationing 140,000 troops on the border with Afghanistan, an effort to normalize support for the Pakistani military after nearly two years of crises and mutual retaliation.

The biggest proponent of putting foreign aid and military reimbursements to Pakistan on a steady footing is the man President Barack Obama is leaning toward naming as secretary of state: Senator John Kerry, Democrat of Massachusetts. Mr. Kerry, the chairman of the Senate Foreign Relations Committee, has frequently served as an envoy to Pakistan, including after the killing of Osama bin Laden, and was a co-author of a law that authorized five years and about $7.5 billion of nonmilitary assistance to Pakistan.

The United States also provides about $2 billion in annual security assistance, roughly half of which goes to reimburse Pakistan for conducting military operations to fight terrorism.

Until now, many of these reimbursements, called coalition support funds, have been held up, in part because of disputes with Pakistan over the Bin Laden raid, the operations of the C.I.A., and its decision to block supply lines into Afghanistan last year.

The $688 million payment — the first since this summer, covering food, ammunition and other expenses from June through November 2011 — has caused barely a ripple of protest since it was sent to Capitol Hill on Dec. 7.

The absence of a reaction, American and Pakistani officials say, underscores how relations between the two countries have been gradually thawing since Pakistan reopened the NATO supply routes in July after an apology from the Obama administration for an errant American airstrike that killed 24 Pakistani soldiers in November 2011.

Mr. Kerry’s nomination would be welcomed in Pakistan, where he is seen as perhaps the most sympathetic to Pakistani concerns of any senior lawmaker. He has nurtured relationships with top civilian and military officials, as well as the I.S.I., Pakistan’s most powerful intelligence agency.

But if he becomes secretary of state, Mr. Kerry will inherit one of the hardest diplomatic tasks in South Asia: helping Pakistan find a role in steering Afghanistan toward a political agreement with the Taliban. As the United States, which tried and failed to broker such an agreement, begins to step back, Pakistan’s role is increasing.

For a relationship rocked in the past two years by a C.I.A. contractor’s shooting of two Pakistanis, the Navy SEAL raid that killed Bin Laden and the accidental airstrike, perhaps the most remarkable event in recent months has been relative calm. A senior American official dealing with Pakistan said recently that “this is the longest we’ve gone in a while without a crisis.”

Sherry Rehman, Pakistan’s ambassador to the United States, said, “Pakistan-United States relations are settling down to a more stable trajectory.”

The interlude has allowed the United States to reduce the huge backlog of NATO supplies at the border — down to about 3,000 containers from 7,000 when the border crossings reopened — and to conduct dry runs for the tons of equipment that will flow out of Afghanistan to Pakistani ports when the American drawdown steps up early next year.

Moreover, the two sides have resumed a series of high-level meetings — capped by Secretary of State Hillary Rodham Clinton’s meeting this month with top Pakistani officials in Brussels — on a range of topics including counterterrorism, economic cooperation, energy and the security of Pakistan’s growing nuclear arsenal.

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Maleeha Lodhi, a former Pakistani ambassador to Washington, concurred. “There’s greater convergence between the two countries than there has been in eight years,” she said. “It’s been a fairly quick kiss and make up, but it’s been driven by the approaching urgency of 2014, and by their shared desire for a stable outcome in the region.”

The one exception to the state of calm has been a tense set of discussions about Pakistan’s nuclear arsenal. United States officials have told their Pakistani colleagues that Islamabad’s move to smaller, more portable weapons creates a greater risk that one could be stolen or diverted. A delegation of American nuclear experts was in Pakistan last week, but found that the two countries had fundamentally divergent views about whether Pakistan’s changes to its arsenal pose a danger.

The greatest progress, officials say, has been in the relationship between Pakistan and Afghanistan, after years of mutual recrimination. A high-level Afghan delegation visited Pakistan in November, resulting in the release of several midlevel Taliban commanders from Pakistani jails as a sign of good will in restarting the peace process.

The United States, which was quietly in the background of those meetings, approved of the release of the prisoners, but has still held back on releasing five militants from Guantánamo Bay, Cuba, a key Taliban demand.

One American official said there was a “big push” to move the talks process forward during the current winter lull in fighting. The United States is quietly seeking to revive a peace channel in Qatar, which was frozen earlier this year after the Taliban refused to participate.

Despite the easing of tensions in recent months, there are still plenty of sore spots in the relationship.

Lt. Gen. Michael D. Barbero, who heads the Pentagon agency responsible for combating roadside bombs, known as improvised explosive devices, or I.E.D.’s, told a Senate hearing last week that Pakistan’s efforts to stem the flow of a common agricultural fertilizer, calcium ammonium nitrate, that Taliban insurgents use to make roadside bombs had fallen woefully short.

“Our Pakistani partners can and must do more,” General Barbero told a Senate Foreign Relations subcommittee hearing.

American officials have also all but given up on Pakistan’s carrying out a clearing operation in North Waziristan, a major militant safe haven.

“Pakistan’s continued acceptance of sanctuaries for Afghan-focused insurgents and failure to interdict I.E.D. materials and components continue to undermine the security of Afghanistan and pose an enduring threat to U.S., coalition and Afghan forces,” a Pentagon report, mandated by Congress, concluded last week.

Declan Walsh contributed reporting from Islamabad, Pakistan.

A version of this article appears in print on December 18, 2012, on Page A9 of the New York edition with the headline: In Sign of Normalization, Pentagon To Reimburse Pakistan $688 Million. Order Reprints|Today's Paper|Subscribe